Samples were genotyped on the Illumina Human 1 M beadchip at the Center for Inherited Diseases Research at Johns Hopkins University. Details of quality control procedures have been previously reported [25]. Analysis was restricted to SNPs with minor allele frequency ≥ 1%, call rate ≥ 98% and Hardy-Weinberg Equilibrium p-value ≥ 10−5. IMPUTE2 was used to phase the observed genotypes and impute unobserved genotypes [28, 29] using the 1000 Genomes phase 1 reference panel (release June 2011, b37) [30] separately by ancestry. To minimize effects of population stratification, 577,039 SNPs were used to generate ten principal components (PC) using EIGENSOFT 3.0 [31] and SMARTPCA [32]. To circumvent over-fitting only PCs that were associated with BMI and indicative of ancestral background were used in subsequent analyses [31–33]. The software Quanto was used to assess the power of the SAGE sample (n = 2,348) to detect known BMI/obesity genetic variants [34]. These calculations were computed using descriptive statistics reported in original papers, which included variant frequency, effect size, odds-ratio and percent variance accounted for.
